Skip to main content

Natural Products Linker

Project description

Badges

fair-software.eu recommendations
(1/5) code repository github repo badge
(2/5) license github license badge
(3/5) community registry pypi badge
(4/5) citation Zenodo
(5/5) checklist OpenSSF Scorecard
overall fair-software badge
Other best practices
Documentation Static Badge 🔗
Build & Test build
Static analysis workflow scq badge
Coverage workflow scc badge
Citation data consistency cffconvert

Natural Products Linker (NPLinker)

NPLinker is a python framework for data mining microbial natural products by integrating genomics and metabolomics data.

Original paper: Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Setup and usage

Requirement

Installation

NPLinker is a python package, using both pypi packages and non-pypi packages as dependencies. It requires ~4.5GB of disk space to install all the dependencies.

# Check python version (requiring ≥3.9)
python --version

# Create a new virtual environment
python -m venv env
source env/bin/activate

# install from nplinker releases (requiring ~300MB of disk space)
pip install --pre nplinker

# or install the latest from source code
pip install git+https://github.com/nplinker/nplinker@dev 

# install nplinker non-pypi dependencies and databases (~4GB)
install-nplinker-deps

A virtual environment is required to install the the non-pypi dependencies. You can also use conda to manage python environments.

Testing

To run the tests, you need to clone this repo and install the development dependencies:

# Create a new virtual environment
python -m venv env
source env/bin/activate

# Clone the repository and install the development dependencies
git clone https://github.com/NPLinker/nplinker.git
cd nplinker
pip install -e ".[dev]"
install-nplinker-deps

Unit tests

To run the unit tests, you can use the following command:

pytest

Pytest will use all available CPU cores to run the unit tests in parallel.

Integration tests

To run the integration tests, you can use the following command:

pytest -n1 tests/integration

The -n1 is to use one CPU core to run the tests. Change it to -n2 if you want to use two CPU cores to run in parallel.

Usage

See the documentation for more information about how to use NPLinker.

Contributing

If you want to contribute to the development of nplinker, have a look at the contribution guidelines and README for developers.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

nplinker-2.0.0a6.tar.gz (6.0 MB view details)

Uploaded Source

Built Distribution

nplinker-2.0.0a6-py3-none-any.whl (6.1 MB view details)

Uploaded Python 3

File details

Details for the file nplinker-2.0.0a6.tar.gz.

File metadata

  • Download URL: nplinker-2.0.0a6.tar.gz
  • Upload date:
  • Size: 6.0 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.10.13

File hashes

Hashes for nplinker-2.0.0a6.tar.gz
Algorithm Hash digest
SHA256 2e2a4546c481170d6faa382e2e1c0e1ea4b7b94e1db1c72f24ab217bc7192b61
MD5 c92ab97d5e849aa9c24a5ae1be7d339e
BLAKE2b-256 63bd22d89d45b5dddc6be8c6f0e07384194078adf9a7687e693283c7669c1650

See more details on using hashes here.

Provenance

File details

Details for the file nplinker-2.0.0a6-py3-none-any.whl.

File metadata

  • Download URL: nplinker-2.0.0a6-py3-none-any.whl
  • Upload date:
  • Size: 6.1 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.10.13

File hashes

Hashes for nplinker-2.0.0a6-py3-none-any.whl
Algorithm Hash digest
SHA256 fb857ddbcb60e388196692ac1eed769b7ab1e90ceb60665f10bce26e564874b2
MD5 fdae767c799583f04a4a5d9c2bd12c6b
BLAKE2b-256 fba40a4ad0a8e9fcef74b25c7ead38a5c5d9d54873f44b5d656d20655c7734a0

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page